Placing individual molecules in the center of nanoapertures.

While nanophotonic devices are unfolding their potential for single-molecule fluorescence studies, metallic quenching and steric hindrance, occurring within these structures, raise the desire for site-specific immobilization of the molecule of interest. Here, we refine the single-molecule cut-and-paste technique by optical superresolution routines to immobilize single fluorescent molecules in the center of nanoapertures. By comparing their fluorescence lifetime and intensity to stochastically immobilized fluorophores, we characterize the electrodynamic environment in these nanoapertures and proof the nanometer precision of our loading method.

Effects of cytosine hydroxymethylation on DNA strand separation.

Cytosine hydroxymethylation is an epigenetic control factor in higher organisms. New discoveries of the biological roles of hydroxymethylation serve to raise questions about how this epigenetic modification exerts its functions and how organisms discriminate cytosine hydroxymethylation from methylation. Here, we report investigations that reveal an effect of cytosine hydroxymethylation on mechanical properties of DNA under load.

Peptide-antibody complex as handle for single-molecule cut & paste.

Molecule-by-molecule arrangement of proteins, for example, in enzymatic networks of predefined composition and proximity, is a major goal that may be accomplished by the single-molecule cut-and-paste technique (SMC&P). For this purpose, co-expressed anchors and handles as protein tags should be employed. As a first step in this direction, the authors develop an SMC&P design which exploits an antibody-peptide complex as a molecular handle.

Cytosine methylation alters DNA mechanical properties.

DNA methylation plays an essential role in transcriptional control of organismal development in epigenetics, from turning off a specific gene to inactivation of entire chromosomes. While the biological function of DNA methylation is becoming increasingly clear, the mechanism of methylation-induced gene regulation is still poorly understood. Through single-molecule force experiments and simulation we investigated the effects of methylation on strand separation of DNA, a crucial step in gene expression.

A high throughput molecular force assay for protein-DNA interactions.

An accurate and genome-wide characterization of protein-DNA interactions such as transcription factor binding is of utmost importance for modern biology. Powerful screening methods emerged. But the vast majority of these techniques depend on special labels or markers against the ligand of interest and moreover most of them are not suitable for detecting low-affinity binders.